Starting phenix.real_space_refine on Thu Mar 5 14:16:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b8p_12088/03_2026/7b8p_12088.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b8p_12088/03_2026/7b8p_12088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b8p_12088/03_2026/7b8p_12088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b8p_12088/03_2026/7b8p_12088.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b8p_12088/03_2026/7b8p_12088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b8p_12088/03_2026/7b8p_12088.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 15000 2.51 5 N 3774 2.21 5 O 4293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23202 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Chain: "B" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Chain: "C" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7734 Classifications: {'peptide': 1015} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 968} Chain breaks: 1 Time building chain proxies: 4.09, per 1000 atoms: 0.18 Number of scatterers: 23202 At special positions: 0 Unit cell: (119.7, 112.35, 138.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4293 8.00 N 3774 7.00 C 15000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 978.7 milliseconds 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 24 sheets defined 59.0% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.951A pdb=" N ARG A 7 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 27 removed outlier: 3.611A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.515A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 360 Processing helix chain 'A' and resid 361 through 370 Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 423 removed outlier: 4.328A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.777A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'A' and resid 461 through 496 removed outlier: 4.089A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 512 through 534 removed outlier: 3.768A pdb=" N HIS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 698 Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 747 removed outlier: 3.596A pdb=" N VAL A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU A 867 " --> pdb=" O GLN A 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 868 " --> pdb=" O MET A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 Processing helix chain 'A' and resid 895 through 911 Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.784A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 982 removed outlier: 4.610A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.612A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.514A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 360 Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.327A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.777A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 461 through 496 removed outlier: 4.089A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 512 through 534 removed outlier: 3.767A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP B 642 " --> pdb=" O LYS B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 698 Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 747 removed outlier: 3.634A pdb=" N VAL B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER B 747 " --> pdb=" O THR B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 841 Processing helix chain 'B' and resid 852 through 862 Processing helix chain 'B' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU B 867 " --> pdb=" O GLN B 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 868 " --> pdb=" O MET B 864 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 Processing helix chain 'B' and resid 895 through 911 Processing helix chain 'B' and resid 915 through 946 removed outlier: 3.783A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 982 removed outlier: 4.610A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1022 removed outlier: 4.122A pdb=" N VAL B1014 " --> pdb=" O PHE B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.951A pdb=" N ARG C 7 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 27 removed outlier: 3.612A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.855A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.515A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 360 Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.328A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 409 " --> pdb=" O ILE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 453 removed outlier: 6.281A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.775A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 461 through 496 removed outlier: 4.090A pdb=" N GLN C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 512 through 534 removed outlier: 3.767A pdb=" N HIS C 534 " --> pdb=" O LYS C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 580 through 595 Processing helix chain 'C' and resid 635 through 646 removed outlier: 3.651A pdb=" N ASP C 642 " --> pdb=" O LYS C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 698 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 747 removed outlier: 3.634A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER C 747 " --> pdb=" O THR C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 773 through 778 removed outlier: 3.973A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 841 Processing helix chain 'C' and resid 852 through 862 Processing helix chain 'C' and resid 863 through 884 removed outlier: 3.574A pdb=" N LEU C 867 " --> pdb=" O GLN C 863 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 868 " --> pdb=" O MET C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 894 Processing helix chain 'C' and resid 895 through 911 Processing helix chain 'C' and resid 915 through 946 removed outlier: 3.783A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 982 removed outlier: 4.611A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 986 through 1007 removed outlier: 4.168A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1022 removed outlier: 4.121A pdb=" N VAL C1014 " --> pdb=" O PHE C1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 821 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N MET A 706 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.678A pdb=" N GLN A 42 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET A 138 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.832A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 605 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 572 " --> pdb=" O MET A 656 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS A 182 " --> pdb=" O GLN A 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE A 763 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N MET A 184 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN A 765 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A 186 " --> pdb=" O GLN A 765 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 796 through 803 removed outlier: 8.353A pdb=" N SER B 235 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE A 718 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 781 through 783 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 821 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.831A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 605 " --> pdb=" O PHE B 623 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 572 " --> pdb=" O MET B 656 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 803 removed outlier: 8.349A pdb=" N SER C 235 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 718 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 127 through 132 removed outlier: 4.677A pdb=" N GLN C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.622A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 3.831A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 605 " --> pdb=" O PHE C 623 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER C 572 " --> pdb=" O MET C 656 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.776A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 783 1563 hydrogen bonds defined for protein. 4545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7320 1.34 - 1.46: 4193 1.46 - 1.58: 11836 1.58 - 1.70: 6 1.70 - 1.81: 264 Bond restraints: 23619 Sorted by residual: bond pdb=" CA LEU B 198 " pdb=" C LEU B 198 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.36e-02 5.41e+03 2.44e+01 bond pdb=" CA LEU C 198 " pdb=" C LEU C 198 " ideal model delta sigma weight residual 1.526 1.593 -0.067 1.36e-02 5.41e+03 2.43e+01 bond pdb=" CA LEU A 198 " pdb=" C LEU A 198 " ideal model delta sigma weight residual 1.526 1.591 -0.066 1.36e-02 5.41e+03 2.34e+01 bond pdb=" CA VAL C 259 " pdb=" CB VAL C 259 " ideal model delta sigma weight residual 1.533 1.482 0.052 1.13e-02 7.83e+03 2.09e+01 bond pdb=" CA VAL A 259 " pdb=" CB VAL A 259 " ideal model delta sigma weight residual 1.533 1.482 0.051 1.13e-02 7.83e+03 2.07e+01 ... (remaining 23614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 31637 3.33 - 6.67: 331 6.67 - 10.00: 48 10.00 - 13.33: 15 13.33 - 16.66: 6 Bond angle restraints: 32037 Sorted by residual: angle pdb=" N LYS A 226 " pdb=" CA LYS A 226 " pdb=" C LYS A 226 " ideal model delta sigma weight residual 110.35 98.53 11.82 1.40e+00 5.10e-01 7.13e+01 angle pdb=" N LYS B 226 " pdb=" CA LYS B 226 " pdb=" C LYS B 226 " ideal model delta sigma weight residual 110.35 98.58 11.77 1.40e+00 5.10e-01 7.07e+01 angle pdb=" N LYS C 226 " pdb=" CA LYS C 226 " pdb=" C LYS C 226 " ideal model delta sigma weight residual 110.35 98.61 11.74 1.40e+00 5.10e-01 7.04e+01 angle pdb=" N LYS B 254 " pdb=" CA LYS B 254 " pdb=" C LYS B 254 " ideal model delta sigma weight residual 110.80 127.46 -16.66 2.13e+00 2.20e-01 6.12e+01 angle pdb=" N LYS C 254 " pdb=" CA LYS C 254 " pdb=" C LYS C 254 " ideal model delta sigma weight residual 110.80 127.45 -16.65 2.13e+00 2.20e-01 6.11e+01 ... (remaining 32032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.70: 12519 15.70 - 31.41: 1336 31.41 - 47.11: 353 47.11 - 62.81: 93 62.81 - 78.52: 24 Dihedral angle restraints: 14325 sinusoidal: 5553 harmonic: 8772 Sorted by residual: dihedral pdb=" CA TYR B 49 " pdb=" C TYR B 49 " pdb=" N PRO B 50 " pdb=" CA PRO B 50 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR C 49 " pdb=" C TYR C 49 " pdb=" N PRO C 50 " pdb=" CA PRO C 50 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR A 49 " pdb=" C TYR A 49 " pdb=" N PRO A 50 " pdb=" CA PRO A 50 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 14322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3287 0.071 - 0.142: 457 0.142 - 0.212: 96 0.212 - 0.283: 9 0.283 - 0.354: 3 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA VAL B 707 " pdb=" N VAL B 707 " pdb=" C VAL B 707 " pdb=" CB VAL B 707 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA VAL C 707 " pdb=" N VAL C 707 " pdb=" C VAL C 707 " pdb=" CB VAL C 707 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA VAL A 707 " pdb=" N VAL A 707 " pdb=" C VAL A 707 " pdb=" CB VAL A 707 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3849 not shown) Planarity restraints: 4032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 35 " -0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO C 36 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO C 36 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 36 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 35 " 0.061 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO B 36 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 35 " 0.061 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 36 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 36 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 36 " 0.049 5.00e-02 4.00e+02 ... (remaining 4029 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 10123 2.92 - 3.41: 24347 3.41 - 3.91: 38792 3.91 - 4.40: 45193 4.40 - 4.90: 75260 Nonbonded interactions: 193715 Sorted by model distance: nonbonded pdb=" O GLU A 225 " pdb=" C LYS A 226 " model vdw 2.425 3.270 nonbonded pdb=" O GLU B 225 " pdb=" C LYS B 226 " model vdw 2.425 3.270 nonbonded pdb=" O GLU C 225 " pdb=" C LYS C 226 " model vdw 2.425 3.270 nonbonded pdb=" NZ LYS C 931 " pdb=" OD1 ASN C 932 " model vdw 2.466 3.120 nonbonded pdb=" NZ LYS B 931 " pdb=" OD1 ASN B 932 " model vdw 2.466 3.120 ... (remaining 193710 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 21.260 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 23619 Z= 0.313 Angle : 0.972 16.664 32037 Z= 0.648 Chirality : 0.053 0.354 3852 Planarity : 0.006 0.091 4032 Dihedral : 14.537 78.516 8649 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.75 % Allowed : 11.53 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.14), residues: 3033 helix: -1.03 (0.11), residues: 1701 sheet: -2.78 (0.20), residues: 516 loop : -2.59 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 724 TYR 0.017 0.001 TYR C 49 PHE 0.015 0.001 PHE B 917 TRP 0.005 0.001 TRP B 556 HIS 0.002 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00573 (23619) covalent geometry : angle 0.97201 (32037) hydrogen bonds : bond 0.13103 ( 1476) hydrogen bonds : angle 6.91796 ( 4545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 559 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6127 (mm-30) REVERT: A 193 LEU cc_start: 0.8131 (tp) cc_final: 0.7474 (mp) REVERT: A 230 ILE cc_start: 0.9017 (mm) cc_final: 0.8754 (mt) REVERT: A 240 LEU cc_start: 0.8833 (mt) cc_final: 0.8407 (mt) REVERT: A 356 TYR cc_start: 0.7304 (t80) cc_final: 0.6764 (t80) REVERT: A 370 ILE cc_start: 0.9191 (tp) cc_final: 0.8955 (tp) REVERT: A 538 MET cc_start: 0.7943 (mmm) cc_final: 0.7199 (mmt) REVERT: A 743 THR cc_start: 0.8904 (p) cc_final: 0.8696 (p) REVERT: A 824 PHE cc_start: 0.6785 (t80) cc_final: 0.6352 (t80) REVERT: A 835 MET cc_start: 0.9207 (tpt) cc_final: 0.8987 (mmm) REVERT: A 964 PRO cc_start: 0.8897 (Cg_exo) cc_final: 0.8462 (Cg_endo) REVERT: A 1015 PHE cc_start: 0.8535 (m-10) cc_final: 0.8334 (m-80) REVERT: B 32 ILE cc_start: 0.8485 (pt) cc_final: 0.8243 (tt) REVERT: B 234 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8499 (tp) REVERT: B 395 MET cc_start: 0.8502 (mmp) cc_final: 0.8009 (mmp) REVERT: B 647 MET cc_start: 0.8341 (mmm) cc_final: 0.7809 (mmm) REVERT: B 824 PHE cc_start: 0.6754 (t80) cc_final: 0.6429 (t80) REVERT: B 835 MET cc_start: 0.9216 (tpt) cc_final: 0.8938 (tpt) REVERT: B 919 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8381 (mttp) REVERT: B 1015 PHE cc_start: 0.8562 (m-10) cc_final: 0.8193 (m-80) REVERT: C 42 GLN cc_start: 0.8638 (mt0) cc_final: 0.8378 (mt0) REVERT: C 68 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6440 (mm-30) REVERT: C 101 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7076 (mm-30) REVERT: C 352 PHE cc_start: 0.8485 (t80) cc_final: 0.8284 (t80) REVERT: C 356 TYR cc_start: 0.7234 (t80) cc_final: 0.6617 (t80) REVERT: C 370 ILE cc_start: 0.9211 (tp) cc_final: 0.8950 (tp) REVERT: C 393 LEU cc_start: 0.9202 (mt) cc_final: 0.8890 (mt) REVERT: C 395 MET cc_start: 0.8660 (mmp) cc_final: 0.8386 (mmp) REVERT: C 538 MET cc_start: 0.7947 (mmm) cc_final: 0.7676 (mmt) REVERT: C 695 MET cc_start: 0.8505 (tpp) cc_final: 0.8162 (mpp) REVERT: C 759 MET cc_start: 0.9033 (mmt) cc_final: 0.8751 (mmm) REVERT: C 835 MET cc_start: 0.9152 (tpt) cc_final: 0.8789 (tpt) outliers start: 19 outliers final: 1 residues processed: 570 average time/residue: 0.1559 time to fit residues: 138.7111 Evaluate side-chains 363 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 360 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 919 LYS Chi-restraints excluded: chain C residue 919 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 273 GLN A 415 ASN A 574 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 415 ASN ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 805 GLN C 239 GLN C 273 GLN C 415 ASN C 677 GLN ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.120848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.102015 restraints weight = 32842.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.104557 restraints weight = 22118.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.105752 restraints weight = 14399.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.106270 restraints weight = 12271.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.106486 restraints weight = 10872.111| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23619 Z= 0.161 Angle : 0.586 8.029 32037 Z= 0.303 Chirality : 0.042 0.212 3852 Planarity : 0.004 0.057 4032 Dihedral : 4.148 32.088 3193 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.35 % Allowed : 15.06 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.15), residues: 3033 helix: 0.48 (0.12), residues: 1710 sheet: -3.07 (0.21), residues: 456 loop : -1.47 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 724 TYR 0.016 0.002 TYR A 78 PHE 0.027 0.002 PHE C1015 TRP 0.015 0.001 TRP A 708 HIS 0.003 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00372 (23619) covalent geometry : angle 0.58550 (32037) hydrogen bonds : bond 0.04292 ( 1476) hydrogen bonds : angle 4.99867 ( 4545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 373 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 ILE cc_start: 0.9145 (tp) cc_final: 0.8866 (tp) REVERT: A 426 SER cc_start: 0.8689 (m) cc_final: 0.8385 (p) REVERT: A 538 MET cc_start: 0.7962 (mmm) cc_final: 0.7687 (mmt) REVERT: A 539 MET cc_start: 0.8499 (tpp) cc_final: 0.8250 (mmm) REVERT: A 825 ASP cc_start: 0.6929 (m-30) cc_final: 0.6487 (m-30) REVERT: A 835 MET cc_start: 0.9290 (tpt) cc_final: 0.8820 (tpt) REVERT: B 68 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6937 (mm-30) REVERT: B 102 MET cc_start: 0.8261 (tpt) cc_final: 0.7464 (mmt) REVERT: B 193 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8210 (mt) REVERT: B 527 MET cc_start: 0.7488 (ttt) cc_final: 0.7189 (mtp) REVERT: B 647 MET cc_start: 0.8346 (mmm) cc_final: 0.8013 (mmm) REVERT: B 745 MET cc_start: 0.6276 (mmm) cc_final: 0.5905 (mmm) REVERT: B 825 ASP cc_start: 0.6636 (m-30) cc_final: 0.6420 (m-30) REVERT: B 835 MET cc_start: 0.9207 (tpt) cc_final: 0.8579 (tpt) REVERT: B 864 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6640 (tpp) REVERT: B 1015 PHE cc_start: 0.8551 (m-10) cc_final: 0.8130 (m-80) REVERT: C 26 SER cc_start: 0.9155 (t) cc_final: 0.8868 (p) REVERT: C 42 GLN cc_start: 0.8649 (mt0) cc_final: 0.8270 (mt0) REVERT: C 68 GLU cc_start: 0.7256 (mm-30) cc_final: 0.7036 (mm-30) REVERT: C 91 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8159 (m) REVERT: C 101 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6716 (mm-30) REVERT: C 254 LYS cc_start: 0.7656 (tppt) cc_final: 0.7442 (tppt) REVERT: C 356 TYR cc_start: 0.7310 (t80) cc_final: 0.6605 (t80) REVERT: C 370 ILE cc_start: 0.9198 (tp) cc_final: 0.8914 (tp) REVERT: C 420 MET cc_start: 0.7627 (mtp) cc_final: 0.7327 (mtp) REVERT: C 538 MET cc_start: 0.8176 (mmm) cc_final: 0.7900 (mmt) REVERT: C 691 GLN cc_start: 0.8541 (tt0) cc_final: 0.8135 (tt0) REVERT: C 695 MET cc_start: 0.8413 (mpp) cc_final: 0.7910 (mpp) REVERT: C 745 MET cc_start: 0.5968 (mmm) cc_final: 0.5598 (mmm) REVERT: C 759 MET cc_start: 0.9070 (mmt) cc_final: 0.8844 (mmm) REVERT: C 839 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8695 (mt) REVERT: C 1015 PHE cc_start: 0.8598 (m-80) cc_final: 0.8209 (m-80) outliers start: 60 outliers final: 32 residues processed: 419 average time/residue: 0.1376 time to fit residues: 96.2649 Evaluate side-chains 362 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 326 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 864 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 258 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 GLN B 574 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.099844 restraints weight = 33169.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.102605 restraints weight = 19157.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.104454 restraints weight = 13169.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105696 restraints weight = 10250.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.106481 restraints weight = 8614.599| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23619 Z= 0.186 Angle : 0.571 7.503 32037 Z= 0.292 Chirality : 0.042 0.152 3852 Planarity : 0.004 0.054 4032 Dihedral : 3.994 19.811 3183 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.14 % Allowed : 15.84 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 3033 helix: 1.04 (0.13), residues: 1710 sheet: -2.23 (0.22), residues: 504 loop : -1.26 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 724 TYR 0.017 0.001 TYR B 157 PHE 0.021 0.002 PHE C 824 TRP 0.010 0.001 TRP C 708 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00436 (23619) covalent geometry : angle 0.57100 (32037) hydrogen bonds : bond 0.04053 ( 1476) hydrogen bonds : angle 4.83772 ( 4545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 345 time to evaluate : 0.828 Fit side-chains REVERT: A 26 SER cc_start: 0.9154 (t) cc_final: 0.8705 (p) REVERT: A 370 ILE cc_start: 0.9171 (tp) cc_final: 0.8893 (tp) REVERT: A 383 MET cc_start: 0.8774 (mtp) cc_final: 0.8552 (mtp) REVERT: A 426 SER cc_start: 0.8565 (m) cc_final: 0.8236 (p) REVERT: A 538 MET cc_start: 0.7923 (mmm) cc_final: 0.7615 (mmt) REVERT: A 592 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: A 684 MET cc_start: 0.9188 (mmt) cc_final: 0.8710 (tpt) REVERT: A 824 PHE cc_start: 0.6516 (t80) cc_final: 0.6255 (t80) REVERT: A 883 TYR cc_start: 0.7284 (m-10) cc_final: 0.7029 (m-10) REVERT: B 68 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6977 (mm-30) REVERT: B 102 MET cc_start: 0.8198 (tpt) cc_final: 0.7152 (mmt) REVERT: B 348 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7440 (tmm) REVERT: B 592 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: B 824 PHE cc_start: 0.6316 (t80) cc_final: 0.6069 (t80) REVERT: B 838 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8672 (mp) REVERT: B 839 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8788 (mp) REVERT: B 864 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6684 (tpp) REVERT: B 1015 PHE cc_start: 0.8521 (m-10) cc_final: 0.8115 (m-80) REVERT: C 26 SER cc_start: 0.9114 (t) cc_final: 0.8853 (p) REVERT: C 42 GLN cc_start: 0.8627 (mt0) cc_final: 0.8322 (mt0) REVERT: C 101 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6981 (mm-30) REVERT: C 102 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7257 (tpp) REVERT: C 157 TYR cc_start: 0.8849 (t80) cc_final: 0.8574 (t80) REVERT: C 370 ILE cc_start: 0.9291 (tp) cc_final: 0.8984 (tp) REVERT: C 420 MET cc_start: 0.7532 (mtp) cc_final: 0.7253 (mtp) REVERT: C 538 MET cc_start: 0.8138 (mmm) cc_final: 0.7822 (mmt) REVERT: C 592 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: C 695 MET cc_start: 0.8372 (mpp) cc_final: 0.7737 (mpp) REVERT: C 706 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6898 (mtt) REVERT: C 825 ASP cc_start: 0.6766 (m-30) cc_final: 0.6431 (m-30) REVERT: C 839 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8747 (mt) outliers start: 80 outliers final: 57 residues processed: 407 average time/residue: 0.1308 time to fit residues: 88.0580 Evaluate side-chains 387 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 320 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 864 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 706 MET Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 276 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 180 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.123120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103191 restraints weight = 32573.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.106070 restraints weight = 18653.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.107953 restraints weight = 12702.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.109223 restraints weight = 9823.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.110026 restraints weight = 8195.883| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23619 Z= 0.120 Angle : 0.522 8.079 32037 Z= 0.266 Chirality : 0.040 0.152 3852 Planarity : 0.004 0.053 4032 Dihedral : 3.820 18.393 3183 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.59 % Allowed : 16.98 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 3033 helix: 1.45 (0.13), residues: 1707 sheet: -1.71 (0.23), residues: 477 loop : -1.07 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 67 TYR 0.019 0.001 TYR B 157 PHE 0.020 0.001 PHE B 824 TRP 0.015 0.001 TRP A 512 HIS 0.001 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00261 (23619) covalent geometry : angle 0.52164 (32037) hydrogen bonds : bond 0.03605 ( 1476) hydrogen bonds : angle 4.59366 ( 4545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 371 time to evaluate : 0.848 Fit side-chains REVERT: A 26 SER cc_start: 0.9143 (t) cc_final: 0.8756 (p) REVERT: A 370 ILE cc_start: 0.9173 (tp) cc_final: 0.8856 (tp) REVERT: A 426 SER cc_start: 0.8571 (m) cc_final: 0.8241 (p) REVERT: A 745 MET cc_start: 0.5654 (mmm) cc_final: 0.5440 (mmm) REVERT: A 839 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8644 (mp) REVERT: A 876 PHE cc_start: 0.8896 (t80) cc_final: 0.8543 (t80) REVERT: B 26 SER cc_start: 0.9095 (t) cc_final: 0.8894 (p) REVERT: B 68 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 101 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6681 (mm-30) REVERT: B 102 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7106 (mmt) REVERT: B 240 LEU cc_start: 0.8942 (mt) cc_final: 0.8554 (mp) REVERT: B 348 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6894 (mtt) REVERT: B 527 MET cc_start: 0.7472 (ttt) cc_final: 0.7166 (ttp) REVERT: B 864 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6644 (tpt) REVERT: B 893 MET cc_start: 0.7334 (mmp) cc_final: 0.7041 (mtp) REVERT: B 1015 PHE cc_start: 0.8533 (m-10) cc_final: 0.8156 (m-80) REVERT: C 26 SER cc_start: 0.9078 (t) cc_final: 0.8823 (p) REVERT: C 42 GLN cc_start: 0.8542 (mt0) cc_final: 0.8205 (mt0) REVERT: C 91 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8095 (m) REVERT: C 101 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7048 (mm-30) REVERT: C 157 TYR cc_start: 0.8798 (t80) cc_final: 0.8533 (t80) REVERT: C 370 ILE cc_start: 0.9265 (tp) cc_final: 0.8948 (tp) REVERT: C 393 LEU cc_start: 0.9170 (mt) cc_final: 0.8961 (mt) REVERT: C 538 MET cc_start: 0.8038 (mmm) cc_final: 0.7764 (mmt) REVERT: C 691 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: C 695 MET cc_start: 0.8387 (tpp) cc_final: 0.7753 (mpp) REVERT: C 839 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8758 (mt) REVERT: C 1015 PHE cc_start: 0.8644 (m-80) cc_final: 0.8362 (m-80) outliers start: 66 outliers final: 41 residues processed: 416 average time/residue: 0.1281 time to fit residues: 88.6615 Evaluate side-chains 379 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 331 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 864 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 691 GLN Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 285 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 216 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 235 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.122800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.102936 restraints weight = 32624.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105746 restraints weight = 18811.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107620 restraints weight = 12952.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.108873 restraints weight = 10016.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109761 restraints weight = 8372.334| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23619 Z= 0.128 Angle : 0.527 9.051 32037 Z= 0.267 Chirality : 0.040 0.185 3852 Planarity : 0.004 0.053 4032 Dihedral : 3.793 18.219 3183 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.25 % Allowed : 17.69 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 3033 helix: 1.57 (0.13), residues: 1710 sheet: -1.66 (0.23), residues: 498 loop : -0.81 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 67 TYR 0.019 0.001 TYR B 157 PHE 0.046 0.001 PHE A1015 TRP 0.011 0.001 TRP A 512 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00293 (23619) covalent geometry : angle 0.52662 (32037) hydrogen bonds : bond 0.03549 ( 1476) hydrogen bonds : angle 4.54214 ( 4545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 351 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 26 SER cc_start: 0.9140 (t) cc_final: 0.8804 (p) REVERT: A 102 MET cc_start: 0.6811 (tpp) cc_final: 0.6555 (mmt) REVERT: A 370 ILE cc_start: 0.9225 (tp) cc_final: 0.8914 (tp) REVERT: A 405 ILE cc_start: 0.8555 (mt) cc_final: 0.8352 (mt) REVERT: A 426 SER cc_start: 0.8530 (m) cc_final: 0.8213 (p) REVERT: A 839 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8669 (mp) REVERT: B 26 SER cc_start: 0.9116 (t) cc_final: 0.8901 (p) REVERT: B 68 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7037 (mm-30) REVERT: B 101 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6574 (mm-30) REVERT: B 240 LEU cc_start: 0.8971 (mt) cc_final: 0.8614 (mp) REVERT: B 348 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.6897 (mtt) REVERT: B 527 MET cc_start: 0.7449 (ttt) cc_final: 0.7166 (ttp) REVERT: B 538 MET cc_start: 0.7649 (mmm) cc_final: 0.7406 (mmt) REVERT: B 656 MET cc_start: 0.8254 (tpp) cc_final: 0.8002 (tpt) REVERT: B 839 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8768 (mp) REVERT: B 853 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.7970 (mt) REVERT: B 864 MET cc_start: 0.6967 (tmm) cc_final: 0.6754 (tpt) REVERT: B 1015 PHE cc_start: 0.8547 (m-10) cc_final: 0.8165 (m-80) REVERT: C 26 SER cc_start: 0.9074 (t) cc_final: 0.8838 (p) REVERT: C 42 GLN cc_start: 0.8557 (mt0) cc_final: 0.8255 (mt0) REVERT: C 91 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8154 (m) REVERT: C 101 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6959 (mm-30) REVERT: C 157 TYR cc_start: 0.8794 (t80) cc_final: 0.8478 (t80) REVERT: C 363 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7624 (mtt90) REVERT: C 370 ILE cc_start: 0.9292 (tp) cc_final: 0.8992 (tp) REVERT: C 656 MET cc_start: 0.8378 (tpp) cc_final: 0.7783 (tpt) REVERT: C 695 MET cc_start: 0.8331 (tpp) cc_final: 0.7766 (mpp) REVERT: C 839 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8763 (mt) REVERT: C 1015 PHE cc_start: 0.8591 (m-80) cc_final: 0.8077 (m-80) outliers start: 83 outliers final: 63 residues processed: 412 average time/residue: 0.1312 time to fit residues: 89.4781 Evaluate side-chains 398 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 328 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 594 ASN Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 179 optimal weight: 0.4980 chunk 161 optimal weight: 0.4980 chunk 185 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.120253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.101061 restraints weight = 32932.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103353 restraints weight = 20517.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104448 restraints weight = 14919.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.105897 restraints weight = 11543.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105989 restraints weight = 10288.990| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23619 Z= 0.184 Angle : 0.563 9.432 32037 Z= 0.284 Chirality : 0.042 0.177 3852 Planarity : 0.004 0.051 4032 Dihedral : 3.909 18.045 3183 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.61 % Allowed : 17.88 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 3033 helix: 1.56 (0.13), residues: 1707 sheet: -1.94 (0.22), residues: 546 loop : -0.75 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 67 TYR 0.020 0.001 TYR B 157 PHE 0.035 0.002 PHE B 824 TRP 0.011 0.001 TRP A 512 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00435 (23619) covalent geometry : angle 0.56286 (32037) hydrogen bonds : bond 0.03738 ( 1476) hydrogen bonds : angle 4.64259 ( 4545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 340 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 26 SER cc_start: 0.9130 (t) cc_final: 0.8814 (p) REVERT: A 363 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7382 (mtt90) REVERT: A 370 ILE cc_start: 0.9223 (tp) cc_final: 0.8914 (tp) REVERT: A 405 ILE cc_start: 0.8585 (mt) cc_final: 0.8360 (mt) REVERT: A 426 SER cc_start: 0.8652 (m) cc_final: 0.8288 (p) REVERT: A 592 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: A 656 MET cc_start: 0.8306 (tpt) cc_final: 0.8097 (tpt) REVERT: A 839 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8689 (mp) REVERT: A 876 PHE cc_start: 0.8860 (t80) cc_final: 0.8568 (t80) REVERT: B 26 SER cc_start: 0.9114 (t) cc_final: 0.8898 (p) REVERT: B 68 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 348 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6930 (mtt) REVERT: B 527 MET cc_start: 0.7586 (ttt) cc_final: 0.7266 (ttp) REVERT: B 592 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: B 839 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8748 (mp) REVERT: B 1015 PHE cc_start: 0.8540 (m-10) cc_final: 0.8171 (m-80) REVERT: C 26 SER cc_start: 0.9100 (t) cc_final: 0.8879 (p) REVERT: C 42 GLN cc_start: 0.8694 (mt0) cc_final: 0.8372 (mt0) REVERT: C 91 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8139 (m) REVERT: C 101 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7042 (mm-30) REVERT: C 363 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7681 (mtt90) REVERT: C 370 ILE cc_start: 0.9284 (tp) cc_final: 0.8998 (tp) REVERT: C 592 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: C 656 MET cc_start: 0.8356 (tpp) cc_final: 0.7800 (tpt) REVERT: C 695 MET cc_start: 0.8401 (tpp) cc_final: 0.7769 (mpp) REVERT: C 839 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8754 (mt) REVERT: C 848 TYR cc_start: 0.8554 (p90) cc_final: 0.8239 (p90) REVERT: C 1015 PHE cc_start: 0.8593 (m-80) cc_final: 0.7981 (m-80) outliers start: 92 outliers final: 69 residues processed: 406 average time/residue: 0.1287 time to fit residues: 86.4954 Evaluate side-chains 398 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 319 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 107 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 ASN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.124144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104909 restraints weight = 32632.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.108077 restraints weight = 19211.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109608 restraints weight = 11524.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110040 restraints weight = 9412.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.110175 restraints weight = 8967.333| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23619 Z= 0.131 Angle : 0.543 10.298 32037 Z= 0.273 Chirality : 0.041 0.190 3852 Planarity : 0.004 0.051 4032 Dihedral : 3.874 23.043 3183 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.10 % Allowed : 18.75 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 3033 helix: 1.73 (0.13), residues: 1698 sheet: -1.55 (0.23), residues: 495 loop : -0.71 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 67 TYR 0.020 0.001 TYR B 157 PHE 0.037 0.001 PHE C 824 TRP 0.011 0.001 TRP A 512 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00302 (23619) covalent geometry : angle 0.54310 (32037) hydrogen bonds : bond 0.03485 ( 1476) hydrogen bonds : angle 4.52612 ( 4545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 335 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 26 SER cc_start: 0.9100 (t) cc_final: 0.8796 (p) REVERT: A 89 GLU cc_start: 0.7320 (tt0) cc_final: 0.7071 (tt0) REVERT: A 363 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7323 (mtt90) REVERT: A 370 ILE cc_start: 0.9190 (tp) cc_final: 0.8888 (tp) REVERT: A 391 ASN cc_start: 0.8890 (p0) cc_final: 0.8624 (p0) REVERT: A 405 ILE cc_start: 0.8555 (mt) cc_final: 0.8348 (mt) REVERT: A 426 SER cc_start: 0.8641 (m) cc_final: 0.8264 (p) REVERT: A 835 MET cc_start: 0.9248 (mmm) cc_final: 0.8585 (mmm) REVERT: A 839 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8690 (mp) REVERT: B 68 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 348 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6948 (mtt) REVERT: B 391 ASN cc_start: 0.8933 (p0) cc_final: 0.8712 (p0) REVERT: B 527 MET cc_start: 0.7591 (ttt) cc_final: 0.7261 (ttp) REVERT: B 538 MET cc_start: 0.7659 (mmm) cc_final: 0.7458 (mmt) REVERT: B 539 MET cc_start: 0.8142 (mmm) cc_final: 0.7881 (tpp) REVERT: B 592 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 839 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 853 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8027 (mt) REVERT: B 1015 PHE cc_start: 0.8525 (m-10) cc_final: 0.8180 (m-80) REVERT: C 26 SER cc_start: 0.9096 (t) cc_final: 0.8869 (p) REVERT: C 42 GLN cc_start: 0.8664 (mt0) cc_final: 0.8340 (mt0) REVERT: C 91 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8107 (m) REVERT: C 101 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6967 (mm-30) REVERT: C 157 TYR cc_start: 0.8769 (t80) cc_final: 0.8451 (t80) REVERT: C 363 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7653 (mtt90) REVERT: C 370 ILE cc_start: 0.9268 (tp) cc_final: 0.8982 (tp) REVERT: C 592 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: C 656 MET cc_start: 0.8379 (tpp) cc_final: 0.7768 (tpt) REVERT: C 695 MET cc_start: 0.8400 (tpp) cc_final: 0.7816 (mpp) REVERT: C 839 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8739 (mt) REVERT: C 848 TYR cc_start: 0.8511 (p90) cc_final: 0.8173 (p90) REVERT: C 1015 PHE cc_start: 0.8532 (m-80) cc_final: 0.7867 (m-80) outliers start: 79 outliers final: 64 residues processed: 396 average time/residue: 0.1357 time to fit residues: 88.1005 Evaluate side-chains 393 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 319 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 594 ASN Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 874 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 301 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.120553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.101989 restraints weight = 32442.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.104431 restraints weight = 21236.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.104928 restraints weight = 15235.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.105389 restraints weight = 13413.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.105567 restraints weight = 12174.793| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23619 Z= 0.147 Angle : 0.552 10.131 32037 Z= 0.277 Chirality : 0.041 0.194 3852 Planarity : 0.004 0.050 4032 Dihedral : 3.880 19.257 3183 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.33 % Allowed : 19.06 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 3033 helix: 1.74 (0.13), residues: 1695 sheet: -1.77 (0.22), residues: 537 loop : -0.59 (0.24), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 67 TYR 0.019 0.001 TYR B 157 PHE 0.041 0.001 PHE B 824 TRP 0.011 0.001 TRP C 512 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00344 (23619) covalent geometry : angle 0.55176 (32037) hydrogen bonds : bond 0.03516 ( 1476) hydrogen bonds : angle 4.53245 ( 4545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 330 time to evaluate : 1.469 Fit side-chains REVERT: A 26 SER cc_start: 0.9097 (t) cc_final: 0.8813 (p) REVERT: A 363 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7363 (mtt90) REVERT: A 370 ILE cc_start: 0.9189 (tp) cc_final: 0.8882 (tp) REVERT: A 391 ASN cc_start: 0.8912 (p0) cc_final: 0.8650 (p0) REVERT: A 405 ILE cc_start: 0.8558 (mt) cc_final: 0.8336 (mt) REVERT: A 426 SER cc_start: 0.8670 (m) cc_final: 0.8288 (p) REVERT: A 592 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: A 835 MET cc_start: 0.9252 (mmm) cc_final: 0.8558 (mmm) REVERT: A 839 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8736 (mp) REVERT: B 68 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 348 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6943 (mtt) REVERT: B 391 ASN cc_start: 0.8962 (p0) cc_final: 0.8727 (p0) REVERT: B 527 MET cc_start: 0.7635 (ttt) cc_final: 0.7292 (ttp) REVERT: B 539 MET cc_start: 0.8154 (mmm) cc_final: 0.7926 (tpp) REVERT: B 592 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: B 839 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8752 (mp) REVERT: B 893 MET cc_start: 0.7324 (mmp) cc_final: 0.7009 (mtp) REVERT: B 910 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.8480 (ttt-90) REVERT: B 1015 PHE cc_start: 0.8500 (m-10) cc_final: 0.8155 (m-80) REVERT: C 26 SER cc_start: 0.9105 (t) cc_final: 0.8875 (p) REVERT: C 42 GLN cc_start: 0.8675 (mt0) cc_final: 0.8360 (mt0) REVERT: C 91 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8114 (m) REVERT: C 101 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6991 (mm-30) REVERT: C 363 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7633 (mtt90) REVERT: C 370 ILE cc_start: 0.9290 (tp) cc_final: 0.9058 (tp) REVERT: C 592 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: C 695 MET cc_start: 0.8441 (tpp) cc_final: 0.7813 (mpp) REVERT: C 839 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8718 (mt) outliers start: 85 outliers final: 71 residues processed: 396 average time/residue: 0.1332 time to fit residues: 87.1454 Evaluate side-chains 397 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 316 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 909 SER Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 44 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 233 optimal weight: 0.0980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 823 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.103120 restraints weight = 32573.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106097 restraints weight = 21323.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.107002 restraints weight = 13320.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.107364 restraints weight = 11285.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.107470 restraints weight = 10768.501| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23619 Z= 0.127 Angle : 0.549 10.896 32037 Z= 0.275 Chirality : 0.041 0.175 3852 Planarity : 0.004 0.051 4032 Dihedral : 3.866 25.812 3183 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.29 % Allowed : 19.49 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.16), residues: 3033 helix: 1.81 (0.13), residues: 1695 sheet: -1.71 (0.22), residues: 537 loop : -0.53 (0.24), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 67 TYR 0.020 0.001 TYR B 157 PHE 0.047 0.001 PHE B 824 TRP 0.009 0.001 TRP A 512 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00293 (23619) covalent geometry : angle 0.54950 (32037) hydrogen bonds : bond 0.03409 ( 1476) hydrogen bonds : angle 4.47807 ( 4545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 339 time to evaluate : 0.661 Fit side-chains REVERT: A 26 SER cc_start: 0.9061 (t) cc_final: 0.8795 (p) REVERT: A 363 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7385 (mtt90) REVERT: A 370 ILE cc_start: 0.9168 (tp) cc_final: 0.8900 (tp) REVERT: A 391 ASN cc_start: 0.8903 (p0) cc_final: 0.8629 (p0) REVERT: A 426 SER cc_start: 0.8548 (m) cc_final: 0.8281 (p) REVERT: A 541 ILE cc_start: 0.9018 (mt) cc_final: 0.8764 (tt) REVERT: A 592 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: A 835 MET cc_start: 0.9241 (mmm) cc_final: 0.9015 (mmm) REVERT: A 839 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8722 (mp) REVERT: B 26 SER cc_start: 0.9062 (t) cc_final: 0.8670 (p) REVERT: B 68 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 348 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6918 (mtt) REVERT: B 391 ASN cc_start: 0.8942 (p0) cc_final: 0.8716 (p0) REVERT: B 539 MET cc_start: 0.8105 (mmm) cc_final: 0.7879 (tpp) REVERT: B 592 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: B 839 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8756 (mp) REVERT: B 853 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8032 (mt) REVERT: B 893 MET cc_start: 0.7248 (mmp) cc_final: 0.6988 (mtp) REVERT: B 910 ARG cc_start: 0.8691 (ttt-90) cc_final: 0.8475 (ttt-90) REVERT: B 1015 PHE cc_start: 0.8529 (m-10) cc_final: 0.8156 (m-80) REVERT: C 26 SER cc_start: 0.9087 (t) cc_final: 0.8860 (p) REVERT: C 42 GLN cc_start: 0.8655 (mt0) cc_final: 0.8334 (mt0) REVERT: C 91 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8098 (m) REVERT: C 101 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6719 (mm-30) REVERT: C 363 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7626 (mtt90) REVERT: C 370 ILE cc_start: 0.9274 (tp) cc_final: 0.9046 (tp) REVERT: C 592 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: C 656 MET cc_start: 0.8290 (tpp) cc_final: 0.7485 (tpt) REVERT: C 695 MET cc_start: 0.8424 (tpp) cc_final: 0.7799 (mpp) REVERT: C 839 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8730 (mt) REVERT: C 848 TYR cc_start: 0.8501 (p90) cc_final: 0.8116 (p90) REVERT: C 1015 PHE cc_start: 0.8435 (m-80) cc_final: 0.7964 (m-80) outliers start: 84 outliers final: 66 residues processed: 403 average time/residue: 0.1279 time to fit residues: 85.6768 Evaluate side-chains 398 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 321 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 592 GLU Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 942 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 254 optimal weight: 0.0980 chunk 251 optimal weight: 0.0170 chunk 67 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 285 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 overall best weight: 0.3820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105695 restraints weight = 32426.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108476 restraints weight = 20471.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109389 restraints weight = 13044.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.110111 restraints weight = 11256.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.110262 restraints weight = 10401.408| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23619 Z= 0.109 Angle : 0.544 11.431 32037 Z= 0.271 Chirality : 0.040 0.209 3852 Planarity : 0.004 0.052 4032 Dihedral : 3.784 24.276 3183 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.59 % Allowed : 20.24 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.16), residues: 3033 helix: 1.93 (0.13), residues: 1698 sheet: -1.37 (0.23), residues: 495 loop : -0.48 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 67 TYR 0.021 0.001 TYR B 157 PHE 0.043 0.001 PHE A 824 TRP 0.009 0.001 TRP B 708 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00238 (23619) covalent geometry : angle 0.54412 (32037) hydrogen bonds : bond 0.03225 ( 1476) hydrogen bonds : angle 4.36201 ( 4545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6066 Ramachandran restraints generated. 3033 Oldfield, 0 Emsley, 3033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 0.864 Fit side-chains REVERT: A 26 SER cc_start: 0.9052 (t) cc_final: 0.8792 (p) REVERT: A 363 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7344 (mtt90) REVERT: A 370 ILE cc_start: 0.9172 (tp) cc_final: 0.8886 (tp) REVERT: A 391 ASN cc_start: 0.8931 (p0) cc_final: 0.8630 (p0) REVERT: A 426 SER cc_start: 0.8527 (m) cc_final: 0.8297 (p) REVERT: A 541 ILE cc_start: 0.8980 (mt) cc_final: 0.8776 (tt) REVERT: A 695 MET cc_start: 0.8231 (tpp) cc_final: 0.7797 (mpp) REVERT: A 839 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8653 (mp) REVERT: B 26 SER cc_start: 0.9021 (t) cc_final: 0.8667 (p) REVERT: B 68 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 240 LEU cc_start: 0.8883 (mt) cc_final: 0.8449 (mp) REVERT: B 348 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6958 (mtt) REVERT: B 391 ASN cc_start: 0.8907 (p0) cc_final: 0.8669 (p0) REVERT: B 592 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7613 (tt0) REVERT: B 839 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8789 (mp) REVERT: B 910 ARG cc_start: 0.8669 (ttt-90) cc_final: 0.8460 (ttt-90) REVERT: B 1015 PHE cc_start: 0.8511 (m-10) cc_final: 0.8156 (m-80) REVERT: C 26 SER cc_start: 0.9037 (t) cc_final: 0.8801 (p) REVERT: C 42 GLN cc_start: 0.8598 (mt0) cc_final: 0.8315 (mt0) REVERT: C 91 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8018 (m) REVERT: C 101 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6994 (mm-30) REVERT: C 157 TYR cc_start: 0.8740 (t80) cc_final: 0.8435 (t80) REVERT: C 363 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7637 (mtt90) REVERT: C 370 ILE cc_start: 0.9277 (tp) cc_final: 0.9055 (tp) REVERT: C 393 LEU cc_start: 0.9150 (mt) cc_final: 0.8922 (mt) REVERT: C 592 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: C 656 MET cc_start: 0.7872 (tpp) cc_final: 0.7580 (tpt) REVERT: C 695 MET cc_start: 0.8365 (tpp) cc_final: 0.7724 (mpp) REVERT: C 839 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8756 (mt) REVERT: C 1001 MET cc_start: 0.8291 (tpt) cc_final: 0.7914 (tpt) REVERT: C 1015 PHE cc_start: 0.8347 (m-80) cc_final: 0.7691 (m-80) outliers start: 66 outliers final: 54 residues processed: 397 average time/residue: 0.1306 time to fit residues: 85.3533 Evaluate side-chains 396 residues out of total 2550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 333 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 GLU Chi-restraints excluded: chain B residue 603 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 732 VAL Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 363 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 603 SER Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 732 VAL Chi-restraints excluded: chain C residue 839 ILE Chi-restraints excluded: chain C residue 853 ILE Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 160 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 208 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 300 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.122554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103760 restraints weight = 32359.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.106335 restraints weight = 21297.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.107419 restraints weight = 13618.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.108081 restraints weight = 11651.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.108258 restraints weight = 10734.766| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23619 Z= 0.135 Angle : 0.563 11.012 32037 Z= 0.278 Chirality : 0.041 0.173 3852 Planarity : 0.004 0.051 4032 Dihedral : 3.816 24.199 3183 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.71 % Allowed : 20.71 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 3033 helix: 1.91 (0.13), residues: 1692 sheet: -1.55 (0.22), residues: 537 loop : -0.41 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 67 TYR 0.021 0.001 TYR B 157 PHE 0.038 0.001 PHE A1015 TRP 0.007 0.001 TRP A 512 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00315 (23619) covalent geometry : angle 0.56342 (32037) hydrogen bonds : bond 0.03338 ( 1476) hydrogen bonds : angle 4.38597 ( 4545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3237.44 seconds wall clock time: 56 minutes 57.21 seconds (3417.21 seconds total)